Knowledge Based Bayesian Segmentation
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This ITK filter is a segmentation algorithm which utilizes Bayes's Rule along with an affine-invarient anisotropic smoothing filter.
I'd like to segment a volume or sub-volume into 'N' classes in a very general manner. I will provide the data and the number of classes that I expect and the algorithm will output a labelmap with 'N' classes.
We have applied this algorithm to 20 normal brain MRI data-sets. We used publicly available data-sets from the Internet Brain Segmentation Repository (IBSR) offered by the Massachusetts General Hospital, Center for Morphometric Analysis. The IBSR data-sets are T1-weighted, 3D coronal brain scans after having been positionally normalized. Manual expert segmentations for these data-sets are publicly available and represent the ground truth used in this work.
This algorithm can be cast in either a static or dynamic framework. In the static framework, the following is the algorithm:
- The user sets the number of distinct classes for segmentation: 'N'
- Generate 'N' prior images (default, 'N' uniform prior images)
- Generate 'N' statistical distributions (default, 'N' normal distributions)
- Generate 'N' membership images by applying the statistical distributions to the raw data
- Generate 'N' posterior images by applying Bayes' rule to the prior and membership images
- Smooth the posterior images for 'm' iterations using an affine-invarient anisotropic smoothing filter and renormalize after each iteration (default, m = 5)
- Apply maximum a posteriori rule to apply labeling and finalize segmentation
In the dynamic framework, the following image depicts the adaptation of the static framework to the dynamic formulation:
The ITK filter design
- Fully incorporated into itkBayesianClassificationImageFilter and itkBayesianClassificationInitializationImageFilter in ITK CVS.
- Fully wrapped in VTK for use in Slicer.
- The working ITK code has been committed to the SandBox
- J. Melonakos, Y. Gao, and A. Tannenbaum. Tissue Tracking: Applications for Brain MRI Classification. SPIE Medical Imaging, 2007.
- J. Melonakos, K. Krishnan, and A. Tannenbaum. An ITK Filter for Bayesian Segmentation: itkBayesianClassifierImageFilter. Insight Journal, 2006.
- J. Melonakos, R. Al-Hakim, J. Fallon, and A. Tannenbaum. Knowledge-Based Segmentation of Brain MRI Scans Using the Insight Toolkit. Insight Journal, 2005.
- John Melonakos @ Georgia Tech
- Yi Gao @ Georgia Tech
- Allen Tannenbaum @ Georgia Tech
- Luis Ibanez @ Kitware
- Karthik Krishnan @ Kitware